Overview

This report summarizes the significant results for rna (FDR < 0.05) of the BlackSheep module, which uses the blacksheepr package for differential extreme value analysis. Briefly, this module counts outliers in user-submitted data, tabulates outliers per group, and runs enrichment analysis (Fisher’s exact test) to identify significant outliers in the groups of interest. More information about the BlackSheep algorithm can be found in Blumenberg et al. (2019, preprint), and detailed documentation of the panoply_blacksheep module can be found here.

Positive outliers (FDR < 0.05)

PAM50

PAM50: Basal

Number of significant genes: 256

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PAM50. Note: row names may not be annotated if there are more than 100 significant genes.

PAM50: Her2

Number of significant genes: 62

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PAM50. Note: row names may not be annotated if there are more than 100 significant genes.

PAM50: LumA

Number of significant genes: 17

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PAM50. Note: row names may not be annotated if there are more than 100 significant genes.

PAM50: LumB

Number of significant genes: 1

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PAM50. Note: row names may not be annotated if there are more than 100 significant genes.

ER.Status

ER.Status: Negative

Number of significant genes: 84

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by ER.Status. Note: row names may not be annotated if there are more than 100 significant genes.

ER.Status: Positive

Number of significant genes: 0

PR.Status

PR.Status: Negative

Number of significant genes: 15

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PR.Status. Note: row names may not be annotated if there are more than 100 significant genes.

PR.Status: Positive

Number of significant genes: 1

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PR.Status. Note: row names may not be annotated if there are more than 100 significant genes.

HER2.Status

HER2.Status: Negative

Number of significant genes: 0

HER2.Status: Positive

Number of significant genes: 31

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by HER2.Status. Note: row names may not be annotated if there are more than 100 significant genes.

TP53.mutation

TP53.mutation: 0

Number of significant genes: 1

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by TP53.mutation. Note: row names may not be annotated if there are more than 100 significant genes.

TP53.mutation: 1

Number of significant genes: 4

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by TP53.mutation. Note: row names may not be annotated if there are more than 100 significant genes.

GATA3.mutation

GATA3.mutation: 0

Number of significant genes: 0

GATA3.mutation: 1

Number of significant genes: 18

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by GATA3.mutation. Note: row names may not be annotated if there are more than 100 significant genes.

Negative outliers (FDR < 0.05)

PAM50

PAM50: Basal

Number of significant genes: 123

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PAM50. Note: row names may not be annotated if there are more than 100 significant genes.

PAM50: Her2

Number of significant genes: 19

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PAM50. Note: row names may not be annotated if there are more than 100 significant genes.

PAM50: LumA

Number of significant genes: 2

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PAM50. Note: row names may not be annotated if there are more than 100 significant genes.

PAM50: LumB

Number of significant genes: 6

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PAM50. Note: row names may not be annotated if there are more than 100 significant genes.

ER.Status

ER.Status: Negative

Number of significant genes: 40

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by ER.Status. Note: row names may not be annotated if there are more than 100 significant genes.

ER.Status: Positive

Number of significant genes: 0

PR.Status

PR.Status: Negative

Number of significant genes: 8

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PR.Status. Note: row names may not be annotated if there are more than 100 significant genes.

PR.Status: Positive

Number of significant genes: 1

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by PR.Status. Note: row names may not be annotated if there are more than 100 significant genes.

HER2.Status

HER2.Status: Negative

Number of significant genes: 0

HER2.Status: Positive

Number of significant genes: 8

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by HER2.Status. Note: row names may not be annotated if there are more than 100 significant genes.

TP53.mutation

TP53.mutation: 0

Number of significant genes: 0

TP53.mutation: 1

Number of significant genes: 6

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by TP53.mutation. Note: row names may not be annotated if there are more than 100 significant genes.

GATA3.mutation

GATA3.mutation: 0

Number of significant genes: 0

GATA3.mutation: 1

Number of significant genes: 12

Table: Significant genes ranked by FDR value.

Figure: Heatmap depicting the fraction of outliers within each significant gene for each sample. Sample annotations are ordered by GATA3.mutation. Note: row names may not be annotated if there are more than 100 significant genes.